A citation-based method for searching scientific literature

Dan Liang, Angela L Elwell, Nil Aygün, Oleh Krupa, Justin M Wolter, Felix A Kyere, Michael J Lafferty, Kerry E Cheek, Kenan P Courtney, Marianna Yusupova, Melanie E Garrett, Allison Ashley-Koch, Gregory E Crawford, Michael I Love, Luis de la Torre-Ubieta, Daniel H Geschwind, Jason L Stein. Nat Neurosci 2021
Times Cited: 3







List of co-cited articles
5 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response.
Kaur Alasoo, Julia Rodrigues, Subhankar Mukhopadhyay, Andrew J Knights, Alice L Mann, Kousik Kundu, Christine Hale, Gordon Dougan, Daniel J Gaffney. Nat Genet 2018
92
66

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
66


Where Are the Disease-Associated eQTLs?
Benjamin D Umans, Alexis Battle, Yoav Gilad. Trends Genet 2021
15
66

RNA splicing is a primary link between genetic variation and disease.
Yang I Li, Bryce van de Geijn, Anil Raj, David A Knowles, Allegra A Petti, David Golan, Yoav Gilad, Jonathan K Pritchard. Science 2016
254
66

iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.
Athanasia D Panopoulos, Matteo D'Antonio, Paola Benaglio, Roy Williams, Sherin I Hashem, Bernhard M Schuldt, Christopher DeBoever, Angelo D Arias, Melvin Garcia, Bradley C Nelson,[...]. Stem Cell Reports 2017
65
33

HMMRATAC: a Hidden Markov ModeleR for ATAC-seq.
Evan D Tarbell, Tao Liu. Nucleic Acids Res 2019
27
33

Snakemake-a scalable bioinformatics workflow engine.
Johannes Köster, Sven Rahmann. Bioinformatics 2018
85
33

ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
Jason D Buenrostro, Beijing Wu, Howard Y Chang, William J Greenleaf. Curr Protoc Mol Biol 2015
33

Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
33

A multi-omic atlas of the human frontal cortex for aging and Alzheimer's disease research.
Philip L De Jager, Yiyi Ma, Cristin McCabe, Jishu Xu, Badri N Vardarajan, Daniel Felsky, Hans-Ulrich Klein, Charles C White, Mette A Peters, Ben Lodgson,[...]. Sci Data 2018
116
33

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis.
Rongbin Zheng, Changxin Wan, Shenglin Mei, Qian Qin, Qiu Wu, Hanfei Sun, Chen-Hao Chen, Myles Brown, Xiaoyan Zhang, Clifford A Meyer,[...]. Nucleic Acids Res 2019
161
33

From reads to insight: a hitchhiker's guide to ATAC-seq data analysis.
Feng Yan, David R Powell, David J Curtis, Nicholas C Wong. Genome Biol 2020
41
33

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
33

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
33

AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis.
Shaopeng Liu, Daofeng Li, Cheng Lyu, Paul M Gontarz, Benpeng Miao, Pamela A F Madden, Ting Wang, Bo Zhang. Genomics Proteomics Bioinformatics 2021
4
33

Dynamic regulation of nucleosome positioning in the human genome.
Dustin E Schones, Kairong Cui, Suresh Cuddapah, Tae-Young Roh, Artem Barski, Zhibin Wang, Gang Wei, Keji Zhao. Cell 2008
912
33

The chromatin accessibility landscape of primary human cancers.
M Ryan Corces, Jeffrey M Granja, Shadi Shams, Bryan H Louie, Jose A Seoane, Wanding Zhou, Tiago C Silva, Clarice Groeneveld, Christopher K Wong, Seung Woo Cho,[...]. Science 2018
284
33

Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia.
Julien Bryois, Melanie E Garrett, Lingyun Song, Alexias Safi, Paola Giusti-Rodriguez, Graham D Johnson, Annie W Shieh, Alfonso Buil, John F Fullard, Panos Roussos,[...]. Nat Commun 2018
55
33

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.
Paul G Giresi, Jonghwan Kim, Ryan M McDaniell, Vishwanath R Iyer, Jason D Lieb. Genome Res 2007
594
33

Genetic effects on liver chromatin accessibility identify disease regulatory variants.
Kevin W Currin, Michael R Erdos, Narisu Narisu, Vivek Rai, Swarooparani Vadlamudi, Hannah J Perrin, Jacqueline R Idol, Tingfen Yan, Ricardo D'Oliveira Albanus, K Alaine Broadaway,[...]. Am J Hum Genet 2021
1
100

High-resolution mapping and characterization of open chromatin across the genome.
Alan P Boyle, Sean Davis, Hennady P Shulha, Paul Meltzer, Elliott H Margulies, Zhiping Weng, Terrence S Furey, Gregory E Crawford. Cell 2008
837
33

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq.
Natsuhiko Kumasaka, Andrew J Knights, Daniel J Gaffney. Nat Genet 2016
82
33

Computational Methods for Assessing Chromatin Hierarchy.
Pearl Chang, Moloya Gohain, Ming-Ren Yen, Pao-Yang Chen. Comput Struct Biotechnol J 2018
12
33

Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures.
Seema B Plaisier, Richard Taschereau, Justin A Wong, Thomas G Graeber. Nucleic Acids Res 2010
183
33

A linear complexity phasing method for thousands of genomes.
Olivier Delaneau, Jonathan Marchini, Jean-François Zagury. Nat Methods 2011
33

New approaches to population stratification in genome-wide association studies.
Alkes L Price, Noah A Zaitlen, David Reich, Nick Patterson. Nat Rev Genet 2010
619
33

An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants.
Joe R Davis, Laure Fresard, David A Knowles, Mauro Pala, Carlos D Bustamante, Alexis Battle, Stephen B Montgomery. Am J Hum Genet 2016
32
33

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies.
Mike A Nalls, Cornelis Blauwendraat, Costanza L Vallerga, Karl Heilbron, Sara Bandres-Ciga, Diana Chang, Manuela Tan, Demis A Kia, Alastair J Noyce, Angli Xue,[...]. Lancet Neurol 2019
392
33

Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data.
Goo Jun, Matthew Flickinger, Kurt N Hetrick, Jane M Romm, Kimberly F Doheny, Gonçalo R Abecasis, Michael Boehnke, Hyun Min Kang. Am J Hum Genet 2012
210
33

Cell culture. Progenitor cells from human brain after death.
T D Palmer, P H Schwartz, P Taupin, B Kaspar, S A Stein, F H Gage. Nature 2001
332
33

Identification of genetic variants associated with alternative splicing using sQTLseekeR.
Jean Monlong, Miquel Calvo, Pedro G Ferreira, Roderic Guigó. Nat Commun 2014
61
33

Developmental disruptions underlying brain abnormalities in ciliopathies.
Jiami Guo, Holden Higginbotham, Jingjun Li, Jackie Nichols, Josua Hirt, Vladimir Ghukasyan, E S Anton. Nat Commun 2015
65
33

Software for computing and annotating genomic ranges.
Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T Morgan, Vincent J Carey. PLoS Comput Biol 2013
33

Second-generation PLINK: rising to the challenge of larger and richer datasets.
Christopher C Chang, Carson C Chow, Laurent Cam Tellier, Shashaank Vattikuti, Shaun M Purcell, James J Lee. Gigascience 2015
33

Conditional eQTL analysis reveals allelic heterogeneity of gene expression.
Rick Jansen, Jouke-Jan Hottenga, Michel G Nivard, Abdel Abdellaoui, Bram Laport, Eco J de Geus, Fred A Wright, Brenda W J H Penninx, Dorret I Boomsma. Hum Mol Genet 2017
70
33


The role of regulatory variation in complex traits and disease.
Frank W Albert, Leonid Kruglyak. Nat Rev Genet 2015
467
33

Tools and best practices for data processing in allelic expression analysis.
Stephane E Castel, Ami Levy-Moonshine, Pejman Mohammadi, Eric Banks, Tuuli Lappalainen. Genome Biol 2015
139
33


Annotation-free quantification of RNA splicing using LeafCutter.
Yang I Li, David A Knowles, Jack Humphrey, Alvaro N Barbeira, Scott P Dickinson, Hae Kyung Im, Jonathan K Pritchard. Nat Genet 2018
170
33

Cancer-upregulated gene 2 (CUG2) overexpression induces apoptosis in SKOV-3 cells.
Sunhee Lee, Wansoo Koh, Hyun-Taek Kim, Cheol-Hee Kim, Soojin Lee. Cell Biochem Funct 2010
5
33

The genetic architecture of the human cerebral cortex.
Katrina L Grasby, Neda Jahanshad, Jodie N Painter, Lucía Colodro-Conde, Janita Bralten, Derrek P Hibar, Penelope A Lind, Fabrizio Pizzagalli, Christopher R K Ching, Mary Agnes B McMahon,[...]. Science 2020
123
33

Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits.
Jian Yang, Teresa Ferreira, Andrew P Morris, Sarah E Medland, Pamela A F Madden, Andrew C Heath, Nicholas G Martin, Grant W Montgomery, Michael N Weedon, Ruth J Loos,[...]. Nat Genet 2012
637
33

Genome-wide analysis of insomnia in 1,331,010 individuals identifies new risk loci and functional pathways.
Philip R Jansen, Kyoko Watanabe, Sven Stringer, Nathan Skene, Julien Bryois, Anke R Hammerschlag, Christiaan A de Leeuw, Jeroen S Benjamins, Ana B Muñoz-Manchado, Mats Nagel,[...]. Nat Genet 2019
185
33

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
33


Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals.
James J Lee, Robbee Wedow, Aysu Okbay, Edward Kong, Omeed Maghzian, Meghan Zacher, Tuan Anh Nguyen-Viet, Peter Bowers, Julia Sidorenko, Richard Karlsson Linnér,[...]. Nat Genet 2018
557
33

Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS.
Amanda Dobbyn, Laura M Huckins, James Boocock, Laura G Sloofman, Benjamin S Glicksberg, Claudia Giambartolomei, Gabriel E Hoffman, Thanneer M Perumal, Kiran Girdhar, Yan Jiang,[...]. Am J Hum Genet 2018
51
33

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.
Naomi R Wray, Stephan Ripke, Manuel Mattheisen, Maciej Trzaskowski, Enda M Byrne, Abdel Abdellaoui, Mark J Adams, Esben Agerbo, Tracy M Air, Till M F Andlauer,[...]. Nat Genet 2018
935
33


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.